Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi5g739 . . . . . Bpe14g01267 . . . . Cma06g01311 Cma14g01824 Car06g01125 Car14g01636 . Cpe08g00344 Cpe03g01527 Bhi01g00709 . . . Hepe05g1670 . . . . . . . . . . . Cone7ag0335 Cone4ag0342 Lsi05g01747 . . Cme06g00475 Blo02g00757 Blo07g00273 Bda11g00641 Bda13g00051 . Bpe13g00547 . Bma06g01607 . Cmo06g01319 Cmo14g01865 . . . . . . . . . . . . . Cla05g00431 Cam05g0469 Cec05g0478 Cco05g0478 Clacu05g0466 Cmu05g0445 Cre05g0506 . Csa03g01193 Chy06g00457 .
Vvi5g740 . . . . . Bpe14g01268 . . . . Cma06g01310 Cma14g01825 Car06g01124 Car14g01637 . Cpe08g00345 Cpe03g01528 Bhi01g00708 . . . Hepe05g1671 . . . . . . . . . . . Cone7ag0336 Cone4ag0343 Lsi05g01748 . . Cme06g00474 Blo02g00758 Blo07g00274 . Bda13g00049 . Bpe13g00546 . Bma06g01608 . Cmo06g01318 Cmo14g01866 . . . . . . . . . . . . . Cla05g00430 Cam05g0468 Cec05g0477 Cco05g0477 Clacu05g0465 Cmu05g0444 Cre05g0505 . Csa03g01192 Chy06g00456 .
Vvi5g741 . . . . . Bpe14g01269 . . . . Cma06g01309 Cma14g01826 Car06g01123 Car14g01638 . Cpe08g00346 Cpe03g01529 Bhi01g00707 . . . Hepe05g1672 . . . . . . . . . Cone14ag0163 Cone15ag0173 . Cone4ag0344 Lsi05g01749 . . Cme06g00473 Blo02g00759 Blo07g00275 Bda11g00642 . . Bpe13g00545 Bma02g00764 Bma06g01609 . Cmo06g01316 Cmo14g01867 . . . . . . . . . . . . . Cla05g00429 Cam05g0467 Cec05g0476 Cco05g0476 Clacu05g0464 Cmu05g0443 Cre05g0504 . Csa03g01191 Chy06g00455 .
Vvi5g742 Blo01g00296 Blo12g00142 Bda03g01088 . . . Bma04g01013 Bma05g01244 . Cmo17g00151 . . . . . . . . . . . . . . Cla06g00678 Cam06g0728 Cec06g0737 Cco06g0745 Clacu06g0720 Cmu06g0704 Cre06g1476 . . . Cone4ag0345 . Csa02g01047 Chy05g00310 . . . . . Bpe05g01099 . . . Sed09g0659 . . . Cma17g00152 . Car17g00134 Cpe12g00129 . Bhi12g01599 Tan06g2391 Cmetu05g1497 . . . Lcy13g0390 . . . . . . . Lsi09g01221 . . Cme05g00584
Vvi5g743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g744 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g745 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g746 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g747 . . . . . Bpe14g01270 . . . . Cma06g01307 Cma14g01828 Car06g01121 Car14g01640 . Cpe08g00348 Cpe03g01531 . . . . . . . . . . . . . . . . . Cone4ag0348 Lsi05g01751 . . Cme06g00471 Blo02g00760 Blo07g00276 . Bda13g00048 . Bpe13g00544 Bma02g00760 Bma06g01610 . Cmo06g01314 Cmo14g01869 . . . . . . . . . . . . . Cla05g00427 Cam05g0465 Cec05g0474 Cco05g0474 Clacu05g0461 Cmu05g0441 Cre05g0502 . Csa03g01189 Chy06g00453 .
Vvi5g748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
3 10963488 10964789 + Bda033512 Bda03g01088 1088
11 6379589 6383026 + Bda005386.3 Bda11g00641 641
11 6387915 6392593 - Bda005387.1 Bda11g00642 642
13 681565 684459 - Bda000890.1 Bda13g00048 48
13 698675 699955 - Bda000891.2 Bda13g00049 49
13 743201 745784 - Bda000897.1 Bda13g00051 51
1 13176136 13180608 + XM_039029780.1 Bhi01g00707 707
1 13180820 13186734 - XM_039040020.1 Bhi01g00708 708
1 13232117 13235999 - XM_039022245.1 Bhi01g00709 709
12 51883039 51885651 - XM_039050832.1 Bhi12g01599 1599
1 3681540 3683382 + BLOR00296 Blo01g00296 296
2 25189375 25195696 + BLOR10487 Blo02g00757 757
2 25209638 25211386 + BLOR10488 Blo02g00758 758
2 25211878 25216773 - BLOR10489 Blo02g00759 759
2 25294900 25297331 + BLOR10490 Blo02g00760 760
7 3224452 3227932 + BLOR18205 Blo07g00273 273
7 3229668 3232222 + BLOR18206 Blo07g00274 274
7 3232581 3237206 - BLOR18207 Blo07g00275 275
7 3252829 3255345 + BLOR18208 Blo07g00276 276
12 9917174 9918431 - BLOR04161 Blo12g00142 142
2 39226439 39229296 - Bma015467.1 Bma02g00760 760
2 39584404 39589273 + Bma015474.1 Bma02g00764 764
4 17784514 17785716 + Bma019629.1 Bma04g01013 1013
5 51808913 51810451 + Bma022435.1 Bma05g01244 1244
6 52240170 52243602 + Bma024722.1 Bma06g01607 1607
6 52245060 52247581 + Bma024723.1 Bma06g01608 1608
6 52250985 52252375 - Bma024724.1 Bma06g01609 1609
6 52269087 52271597 + Bma024725.1 Bma06g01610 1610
5 23405916 23407989 + Bpe018515.1 Bpe05g01099 1099
13 12723507 12725993 - Bpe010248.1 Bpe13g00544 544
13 12731030 12735742 + Bpe010249.1 Bpe13g00545 545
13 12736172 12738662 - Bpe025226 Bpe13g00546 546
13 12739950 12743387 - Bpe010250.1 Bpe13g00547 547
14 9562413 9565884 + Bpe014626.1 Bpe14g01267 1267
14 9567623 9570219 + Bpe025550 Bpe14g01268 1268
14 9570686 9575491 - Bpe014627.2 Bpe14g01269 1269
14 9612794 9615719 + Bpe014628.1 Bpe14g01270 1270
5 4136523 4137916 - CaPI482276_05g004650.1 Cam05g0465 465
5 4168631 4174988 + CaPI482276_05g004670.1 Cam05g0467 467
5 4175073 4181699 - CaPI482276_05g004680.1 Cam05g0468 468
5 4193017 4196499 - CaPI482276_05g004690.1 Cam05g0469 469
6 9844209 9848695 + CaPI482276_06g007280.1 Cam06g0728 728
6 8376873 8380424 - Carg06236-RA Car06g01121 1121
6 8393936 8399687 + Carg06234-RA Car06g01123 1123
6 8400306 8404065 - Carg06233-RA Car06g01124 1124
6 8406802 8410725 - Carg06232-RA Car06g01125 1125
14 13111063 13115127 + Carg16551-RA Car14g01636 1636
14 13117384 13120267 + Carg16550-RA Car14g01637 1637
14 13119109 13125415 - Carg16549-RA Car14g01638 1638
14 13139630 13142799 + Carg16547-RA Car14g01640 1640
17 822355 825675 - Carg10098-RA Car17g00134 134
5 3797834 3799219 - CcPI632755_05g004740.1 Cco05g0474 474
5 3831350 3837832 + CcPI632755_05g004760.1 Cco05g0476 476
5 3838642 3844661 - CcPI632755_05g004770.1 Cco05g0477 477
5 3856841 3860364 - CcPI632755_05g004780.1 Cco05g0478 478
6 8485131 8488735 + CcPI632755_06g007450.1 Cco06g0745 745
5 3789881 3791258 - CePI673135_05g004740.1 Cec05g0474 474
5 3822912 3829383 + CePI673135_05g004760.1 Cec05g0476 476
5 3830194 3836081 - CePI673135_05g004770.1 Cec05g0477 477
5 3847921 3851378 - CePI673135_05g004780.1 Cec05g0478 478
6 8524497 8526911 + CePI673135_06g007370.1 Cec06g0737 737
5 3077855 3080647 - Chy5G093560.1 Chy05g00310 310
6 3021428 3025011 - Chy6G109810.1 Chy06g00453 453
6 3050360 3056444 + Chy6G109830.1 Chy06g00455 455
6 3057243 3061795 - Chy6G109840.1 Chy06g00456 456
6 3067469 3070927 - Chy6G109850.1 Chy06g00457 457
5 3841420 3845004 - ClG42_05g0046100.10 Clacu05g0461 461
5 3876937 3883334 + ClG42_05g0046400.10 Clacu05g0464 464
5 3884141 3890194 - ClG42_05g0046500.10 Clacu05g0465 465
5 3901625 3905109 - ClG42_05g0046600.10 Clacu05g0466 466
6 8400853 8403342 + ClG42_06g0072000.10 Clacu06g0720 720
5 3816421 3821685 - ClCG05G004170.2 Cla05g00427 427
5 3852562 3859534 + ClCG05G004180.1 Cla05g00429 429
5 3859735 3865903 - ClCG05G004190.1 Cla05g00430 430
5 3876994 3881029 - ClCG05G004200.2 Cla05g00431 431
6 8601065 8605128 + ClCG06G007120.1 Cla06g00678 678
6 8641597 8646431 - CmaCh06G013070.1 Cma06g01307 1307
6 8656765 8662071 + CmaCh06G013090.1 Cma06g01309 1309
6 8662020 8665962 - CmaCh06G013100.1 Cma06g01310 1310
6 8668790 8673690 - CmaCh06G013110.1 Cma06g01311 1311
14 13039174 13043387 + CmaCh14G018240.1 Cma14g01824 1824
14 13045553 13048720 + CmaCh14G018250.1 Cma14g01825 1825
14 13048679 13053280 - CmaCh14G018260.1 Cma14g01826 1826
14 13064593 13068829 + CmaCh14G018280.1 Cma14g01828 1828
17 764813 767683 - CmaCh17G001520.1 Cma17g00152 152
5 5924112 5927478 + MELO3C023014.2.1 Cme05g00584 584
6 2967349 2972935 - MELO3C006401.2.1 Cme06g00471 471
6 2995739 3002345 + MELO3C006404.2.1 Cme06g00473 473
6 3002304 3008209 - MELO3C006405.2.1 Cme06g00474 474
6 3011714 3015682 - MELO3C006406.2.1 Cme06g00475 475
5 18055027 18058257 - PI0019528.1 Cmetu05g1497 1497
6 9826153 9832223 - CmoCh06G013140.1 Cmo06g01314 1314
6 9845475 9850760 + CmoCh06G013160.1 Cmo06g01316 1316
6 9851125 9855500 - CmoCh06G013180.1 Cmo06g01318 1318
6 9858800 9863109 - CmoCh06G013190.1 Cmo06g01319 1319
14 14026199 14030174 + CmoCh14G018650.1 Cmo14g01865 1865
14 14032578 14038819 + CmoCh14G018660.1 Cmo14g01866 1866
14 14035929 14040208 - CmoCh14G018670.1 Cmo14g01867 1867
14 14051061 14056094 + CmoCh14G018690.1 Cmo14g01869 1869
17 861747 864723 - CmoCh17G001510.1 Cmo17g00151 151
5 3682196 3682483 - CmPI595203_05g004410.1 Cmu05g0441 441
5 3713071 3719460 + CmPI595203_05g004430.1 Cmu05g0443 443
5 3720267 3726313 - CmPI595203_05g004440.1 Cmu05g0444 444
5 3737746 3741230 - CmPI595203_05g004450.1 Cmu05g0445 445
6 8213133 8215617 + CmPI595203_06g007040.1 Cmu06g0704 704
4 1569566 1572781 + Conep04aG0035400.1 Cone4ag0342 342
4 1573836 1576438 + Conep04aG0035500.1 Cone4ag0343 343
4 1576787 1581477 - Conep04aG0035600.1 Cone4ag0344 344
4 1591520 1593728 + Conep04aG0035700.1 Cone4ag0345 345
4 1595449 1597901 + Conep04aG0036000.1 Cone4ag0348 348
7 1459448 1462583 + Conep07aG0034300.1 Cone7ag0335 335
7 1464750 1467639 + Conep07aG0034400.1 Cone7ag0336 336
14 781217 784400 - Conep14aG0016700.1 Cone14ag0163 163
15 833642 836434 - Conep15aG0017700.1 Cone15ag0173 173
3 11924823 11929041 + Cp4.1LG03g09820.1 Cpe03g01527 1527
3 11932333 11938019 + Cp4.1LG03g09900.1 Cpe03g01528 1528
3 11932903 11938787 - Cp4.1LG03g09800.1 Cpe03g01529 1529
3 11950278 11954490 + Cp4.1LG03g09880.1 Cpe03g01531 1531
8 2135000 2139241 + Cp4.1LG08g03360.1 Cpe08g00344 344
8 2142309 2146330 + Cp4.1LG08g03350.1 Cpe08g00345 345
8 2147057 2153480 - Cp4.1LG08g03310.1 Cpe08g00346 346
8 2168722 2175205 + Cp4.1LG08g03400.1 Cpe08g00348 348
12 821102 824434 - Cp4.1LG12g01370.1 Cpe12g00129 129
5 4476638 4478031 - CrPI670011_05g005020.1 Cre05g0502 502
5 4508573 4515055 + CrPI670011_05g005040.1 Cre05g0504 504
5 4515860 4521835 - CrPI670011_05g005050.1 Cre05g0505 505
5 4533399 4536880 - CrPI670011_05g005060.1 Cre05g0506 506
6 9319201 9321694 + CrPI670011_06g014760.1 Cre06g1476 1476
2 10174786 10178245 - CsaV3_2G012630.1 Csa02g01047 1047
3 9205046 9210365 - CsaV3_3G011890.1 Csa03g01189 1189
3 9232360 9241503 + CsaV3_3G011910.1 Csa03g01191 1191
3 9238568 9244179 - CsaV3_3G011920.1 Csa03g01192 1192
3 9247680 9251646 - CsaV3_3G011930.1 Csa03g01193 1193
5 66578138 66582251 + Hsped.05g16700.1 Hepe05g1670 1670
5 66599713 66607068 + Hsped.05g16710.1 Hepe05g1671 1671
5 66607308 66632875 - Hsped.05g16720.1 Hepe05g1672 1672
13 4443916 4446065 + Maker00023225 Lcy13g0390 390
5 24850832 24854853 + Lsi05G017470.1 Lsi05g01747 1747
5 24865396 24871884 + Lsi05G017480.1 Lsi05g01748 1748
5 24872208 24879671 - Lsi05G017490.1 Lsi05g01749 1749
5 24912925 24918225 + Lsi05G017510.1 Lsi05g01751 1751
9 19624481 19631369 - Lsi09G012210.1 Lsi09g01221 1221
9 8493127 8497195 - Sed0013412.2 Sed09g0659 659
6 76140707 76143327 - Tan0008982.2 Tan06g2391 2391
5 8668793 8672743 + Vvi5g739 Vvi5g739 739
5 8681355 8685240 + Vvi5g740 Vvi5g740 740
5 8695387 8700349 - Vvi5g741 Vvi5g741 741
5 8724660 8727638 + Vvi5g742 Vvi5g742 742
5 8732861 8736105 - Vvi5g743 Vvi5g743 743
5 8742109 8744123 - Vvi5g744 Vvi5g744 744
5 8758142 8760014 + Vvi5g745 Vvi5g745 745
5 8772706 8773778 + Vvi5g746 Vvi5g746 746
5 8773785 8779227 + Vvi5g747 Vvi5g747 747
5 8796211 8801998 + Vvi5g748 Vvi5g748 748
       

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